Behind The Curtains
by Zoja
Summary: A series of missing scenes and vignettes for Stargate: Atlantis. Canon compliant, although with rather clear hints of John/Elizabeth.
1. 4x02 Lifeline

_Disclaimer: I don't own Stargate: Atlantis, Stargate: SG-1 or any of the characters. No profit was made from this work and none will be sought. This is for entertainment purposes only._

 **A/N:** It will be a slightly longer note because I want to say a few things about this series. First of all, the content won't be in chronological order. I have a list of over 20 scenes that I want to write and considering I plan to write them as inspiration hits me, it would be impossible for me to make it chronological, especially that I may actually add more to the list if I come up with something new. That also means that it includes spoilers for the whole show. Secondly, I am planning to stick to canon as much as it is possible, but at the same time, you can expect that there will be more or less obvious hints for John/Elizabeth pairing, as well as references to other, mainly canon pairings. And, finally, I hope you will enjoy it. :)

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 **Episode Reference: 4x02 "Lifeline"**

"If there's a chance she still alive… I'll find her."

"I know" said Sam and a hint of smile appeared on her face as she looked away from the man standing next to her and gazed at the view in front of her.

It was in that moment that she realized how close he actually was with Dr. Weir. He might have been unaware of it himself or simply refused to acknowledge it because of their positions in the city, but the way he spoke about the woman, the determination in his voice as well as the look in his eyes made the fact that he loved as clear as a day to her. Whether anything happened between them or not, or even if his feelings were reciprocated, she wasn't able to say because she hadn't really had much opportunity to watch the two of them together.

She was, of course, aware that the two leaders were one of the most favourite topic of rumours in the city, and even though it was enough to make people think about it, she wasn't going to assume anything. She remembered all too well how the same thing happened to her and the then Colonel O'Neill when they were both in Stargate Command, even though nothing had ever happened between the two of them, except for the unfortunate Za'tarc testing and only a handful of people was aware of what truly occurred during that. She couldn't, however, deny that there was quite a solid foundation for these rumours and she imagined that it was similar in their case.

As she looked at him again, she realized that he probably wasn't even aware just how well she understood him. She had no idea whether he knew about her relationship with Jack, about everything they had gone through. He had never had a chance to actually see the original SG-1 in action as, in contrast to the majority of military personnel of Atlantis, he wasn't a member of any SG-team before going to Pegasus. He most probably heard stories about it during his brief time at the Stargate Command, but he never really struck her as someone, who would really pay attention to them and she imagined his attitude towards them could be the same as hers when it came to everything she heard about his relationship with Elizabeth.

She had actually lost count of how many times over the last decade she had thought that she had lost the man she loved and she had no doubts that the man standing beside her would keep his word and do everything he could to get Dr Weir back. It was, after all, exactly what she had done in all those situations. She had worked practically day and night to bring Jack back to Earth during the months he was trapped on Edora; there was also this time when he was frozen in Antarctica, when she had put everything on the line, blackmailing Weir to let her and Teal'c try to contact Thor, even though they were aware that it would be a one-way-trip and if they didn't manage to get in touch with their Asgard friend, they would never come back to Earth. She would have probably done the very same thing upon finding out about Atlantis falling into the hands of the replicators with Jack and Richard Woolsey getting trapped in the city, if it wasn't for the fact that she was off-world at the time and by the time she returned to Earth, he was already back in Stargate Command safe and sound, greeting her team as they stepped through the gate.

Without another word, she stepped away and walked back into the control room, giving him the privacy that he probably wanted. The balcony didn't really seem like a place to seek it, but when she later found out that it was Dr. Weir's favourite spot in the city and that the two leaders could often be found there together, she perfectly understood why he chose it. Nobody actually voiced this thoughts but as they watched him, they were all pretty sure one of many things going through his head was that he wished she was standing right next to him, enjoying the beautiful view that spread in front of them, and he wasn't the only one.

Sam had never really gotten a chance to get to know Elizabeth Weir very well. She wasn't exactly very keen on befriending the woman during her brief time as the commander of the Stargate Command and even though they later agreed that they wouldn't hold grudges, they never really felt the need to change it. She did, however, hear a lot about her and anyone, whose opinion she actually held in high regard, seemed to think very highly of her leadership, of the work she was doing in Atlantis and she could see it reflected in the way the city's personnel reacted to the loss. It was almost as if Elizabeth was in a way a soul of the expedition, a piece that bound all of them together and she could see they were all finding it difficult to believe she was gone, mourning in their own ways.

She didn't know at the time that it would be her, but as she watched all that, she didn't envy anyone, who would be chosen to be the next leader of Atlantis, the task of replacing Elizabeth Weir. And, as she took one last glance at Sheppard, she could only hope that he would get the chance to fulfil his promise to himself, get her back and maybe even find happiness with her, just like she was allowed to get her happily ever after with Jack O'Neill.


	2. 1x10 The Storm & 1x11 The Eye

**A/N:** Thank you very much for such a great response to the first scene in this story! I hope you will like this one as well! It is a scene that has been floating around in my mind for quite a while now and this series is perfect for sharing it. Also, big thanks to **Loonyloops** for beta-reading.

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 **Episode Reference: 1x10 "The Storm" & 1x11 "The Eye"**

Elizabeth woke up with a gasp and sat up in her bed, pulling her legs to her chest and hiding her face in her hands. Her heart was beating wildly in her chest, her whole body was shaking and she sighed heavily, trying to calm herself down. It wasn't easy, especially since she could practically feel Kolya's grip on her as the man was pulling her towards the Stargate and when she closed her eyes, she could see John aiming his gun in her direction. For a moment, she really thought she was going to die. Even though she now felt a little bad for doubting John, she didn't think he would manage to avoid hitting her as he took a shot at Kolya; the Genii Commander was using her as a shield for a reason, after all. He probably didn't think Sheppard would risk accidentally hurting her. It seemed that they had both underestimated the Major.

It was hardly the first time she had found herself in a dangerous situation but she couldn't remember ever being so shaken up by it. It only seemed to be getting worse, too. She didn't have a chance to think about it earlier; they might have managed to get rid of the Genii, but they still had a city to save and there had been no time for her to dwell on how she felt. Afterwards, when she finally got to her quarters, she couldn't take her mind off everything that had happened. She took a long, hot shower, put on several layers of clothes and covered herself with two blankets as she finally went to bed, but none of it seemed to be working as she couldn't get warm. Eventually, she managed to fall asleep, only to be woken up by the replay of all the events in her dreams.

Groaning with frustration, she kicked the blankets away and got out of the bed. She didn't even bother putting on her robe as she walked out of her quarters; it was the middle of the night and the chance of her running into anyone except for the night shift was practically nonexistent. What she didn't think of was that there could be other people in a similar situation and she had barely walked into the commissary in order to get something to drink, when she almost bumped into John Sheppard, who was on his way out.

"Whoa!" he exclaimed, pulling away from her so that she wouldn't be burnt by the content of the mug he was carrying, and hissed when some of the liquid landed on his skin, letting the cup fall onto the floor.

"Oh God, I'm sorry. You okay?" she asked, catching his wrist to look at his hand and was relieved to see that even though it was a bit red, it didn't look serious.

"Yeah, no worries. I've had worse than that" he said, smiling at her.

It was then that he noticed how exhausted she looked. He was aware that what happened earlier shook her up quite a lot, but it might have been more than he actually realized. He hadn't known what to think about her when they first came to Atlantis, but now he considered her to be one of the strongest people he had ever met and he would sometimes forget that she would often be more affected than anyone else. It was not to say that others didn't care about anything, but as the leader of the city, Elizabeth considered herself personally responsible for everything that happened and he wouldn't be surprised to find out that she blamed herself for the Genii invasion. What worried him more, however, was how she was handling everything that Kolya had put her through.

"Are _you_ okay?" he added, looking at her with concern in his eyes.

"I'm fine" she answered immediately and sighed heavily as she didn't even have to look at him to realize that she did that a little too quickly for it to sound credible and to prevent him from prying.

He decided against it, though. After everything they had gone through, he didn't have to ask to know what was bothering her. He had actually suspected she could be having more difficulties dealing with all of it than she was letting on and as he lied in bed, unable to sleep, he even thought of going to her quarters to check up on her, but figured he should let her rest. That didn't mean that he didn't worry, though. The fact that they were basically the two leaders of the city caused the two of them to spend quite a bit of time together, that in turn had the two of them getting to know each other quite well, and he came to really care about her, thinking of her as probably his closest friend in the city. He really hated to see her suffer like this and wished there was something he could do to make it easier for her, especially after everything she had done for him.

If it wasn't for her, he wouldn't have even come to Atlantis in the first place. He was, of course, aware that none of it would have happened if he didn't possess the strongest ATA gene out of everyone they had tested, but she still chose to disregard his less than perfect record and offered him a chance to prove himself. He knew that Colonel Sumner was entirely against it; the man left him no doubts about that the first chance he got, and it only made him feel more grateful. It was then, that he knew he had made the right decision; even though he didn't know her very well at the time, he was certain that her leadership would be different from what he was used to in the Air Force, something she had proven to him many times by now. A lot of things had changed since they arrived, but one thing hadn't – no matter the circumstances, she still believed in him and even though they didn't always agree about everything, for the first time since he joined the Air Force, he had developed a sense of loyalty and trust for the person whose orders he was following.

This close working relationship that they shared also made him see things that a lot of people wouldn't notice about her simply because she didn't want them to. She had never really confirmed it, but he couldn't help feeling like she was trying to prove herself as the leader of the expedition and because of that, no matter the circumstances, she would do her best not to show any sign of weakness in front of her people, as if it would undermine her position. She also felt responsible for every single person in the city and, even though she would be hiding it behind the mask of an unruffled leader, she was still very affected by all the losses they suffered, probably more than anyone else.

Now, however, not only had they lost people, but they had also came very close to losing the city, not to mention that her own life was threatened as directly as it was possible, and he didn't think that there was anyone who would remain unmoved by all of it. Elizabeth definitely wasn't this sort of a person and even though he initially chose to give her space to deal with everything on her own, he now began to rethink his decision because if he could judge by her appearance, she didn't seem to be coping at all.

"I can't sleep either, so why don't you join me for a cup of hot chocolate?" he asked instead. Knowing that she would probably try to come up with any sort of excuse to escape his company, he didn't really give her a chance to respond before he added: "Would you mind preparing our drinks while I clean the little mess that we've made?"

She just shook her head, abandoning the thought of refusing his invitation and found that it actually felt good to get herself busy with something, even if it was such a trivial task as making two cups of hot chocolate. By the time she was finished, John had already wiped the spilled drink off the floor and surprised her by picking the cups up and motioning his head towards the door. She followed him without a word, although she wasn't sure it was actually a good idea. She didn't really want any company in the first place and this uncertainty only intensified when she realized he was leading her to her quarters. For some reason, however, she seemed unable to voice her objections and it wasn't much later that she found herself sitting on her bed, covered with her quilt, leaning against the wall and holding the steaming mug in her hands, while John settled down at the foot of her bed, facing her.

They sat in silence for a while, sipping their drinks, but in contrast to what she expected, it didn't really feel awkward. She probably shouldn't be surprised by it, considering that they would often find themselves in a similar situation as he seemed to have developed a habit of coming to her office whenever he didn't have anything particular to do or had to work on his share of paperwork, and they would spend hours together without exchanging more than a few words, focused on their respective tasks. What did surprise her, however, was that his presence actually seemed to make her feel better.

"You know…" he eventually spoke, keeping his eyes glued to his drink. "You don't have to be strong all the time. It's been a long, difficult day and nobody is going to think any less of you if you let them see that it had an impact on you. I surely won't."

It was then that she looked up at him, taken aback by his statement. It would be a lie if she claimed that she didn't know what he was talking about because he happened to hit a bull's eye. She didn't say anything but he took it as all the confirmation that he needed and met her gaze as he continued.

"I guess what I'm trying to say is that you don't have to pretend, not in front of me. I've been there, many times, and I know that keeping it bottled up doesn't help. I mean, I'm the last person, who should tell you to talk about it but in case you ever want to talk, and you don't feel like talking to Heightmeyer, I'm here."

He reached his hand out, placing it on hers and gave it a little squeeze. She reciprocated the gesture, accepting his offer and showing her gratitude for it. She had never really been the sort of person, who liked to talk about things that were bothering her, be it something she had difficulty with making up her mind about or an actual, very serious problem; she didn't feel comfortable sharing her thoughts and feelings with people she didn't know about, and she definitely didn't feel like doing it to someone she didn't even know all that well, even if the person came to Atlantis because she believed her to be one of the best psychiatrists in the country. No matter how much she tried, she wouldn't be able to fully understand what Elizabeth was going through, but she felt that if there was anyone, who would, it was John and she really appreciated his offer.

"Thanks" she said, smiling at him.

It was her first truly genuine smile in hours and he was really happy to see it. Lately, he was quite surprised by his own reactions to a lot of things concerning her. This day, however, exceeded everything. It probably wasn't anything unusual to get angry at someone for killing another person, especially if that person was a very important member of the expedition which he was a part of, and also his friend. Even so, it wasn't anger he felt, but an uncontrollable rage that could only be soothed by putting a bullet through the Genii Commander. Though he wasn't about to admit it, this day had taken a toll on all of them.

They sat there for some time longer, talking a bit, although both of them avoided the topic of the invasion. Neither of them was ready to share their feelings about this particular event, but it was this evening that began a tradition of sorts that whenever something would bother either one of them, they would show up in the other's quarters with two mugs of hot chocolate and sit late into the night, talking. It was something he continued even after she was gone as no other place in the city offered him more consolation that her quarters, almost as if her spirit was still there, ready to offer her support.


	3. 3x10 The Return Part 1

**A/N:** Thank you very much for your reviews! They are greatly appreciated! It is really wonderful to read that someone is enjoying this little 'project' of mine. It's been a little longer since the update than last time, but I'm finally adding more. I don't know when the next one's going to be and I don't want to give any promises that I may not be able to keep. Anyway, this part hasn't been beta-read, so beware. It's not exactly a missing scene, as we had gotten something along those lines in the show, but I can't help feeling like it was hardly enough, so I wrote this. Hope you're going to enjoy!

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 **Episode Reference: 3x10 "The Return part 1"**

He couldn't help feeling torn while he walked all over the utilized part of Atlantis, checking up on the progress people made in their preparations to leave the city. There was a part of him that was happy to have something to do as it probably wouldn't take him a lot of time to pack all his belongings, so he would be left with a lot of time and nothing to do but think about how unfair this situation was. At the same time, overseeing the withdrawal was a rather ungrateful job. He really couldn't blame some of the people for temporizing - it was pretty much what he was doing himself, going everywhere except for his own quarters – and he knew they just needed some time, but he still needed to hurry them up, something he didn't like and they didn't appreciate.

By this point, there was only one person that he hadn't checked up on yet and since he didn't find her in her quarters, he was on his way to her office. It was just an excuse, though; he wouldn't be surprised if out of everyone in the city, Elizabeth turned out to be the first one to be ready, but it was a good enough reason to go and see her. It wasn't easy for any of them that they were forced to go back to Earth, but he couldn't help feeling that she was the one taking it the worst. She wouldn't show that, of course; she would suck it up and act like it was just another thing that needed to be done, but he knew her better than to believe this façade. She loved this city, she came to think of it as her home, as a place where she belonged and since he felt the very same way, he had no doubts that it was all much more difficult for her than she was letting on.

It didn't come as a big surprise for him when he found the room empty, save for the box filled with Elizabeth's belongings that was still lying on the desk. It meant that she must have gone somewhere nearby, probably just for a moment, and that left only one place. The sole fact that he had found her on the balcony, staring at the horizon, lost deep in her thoughts, was enough of a confirmation for him that he was right. She didn't even notice his presence until he was standing right by her side, something that was practically impossible to happen under different circumstances. He didn't really know how she did that, but she always seemed to sense his approach and without even glancing in his direction, she would greet him before he made his presence known.

"Hey.." she spoke, smiling at him. Her smile was rather strained and she didn't even try to be subtle about the fact that she wanted to act as if she hadn't almost jumped out of her skin when his arm accidentally brushed against hers, pretending that everything was absolutely normal and fine. "I'm all done with my office and I'll be heading to my quarters right away. I just decided to take advantage of the fact that the Ancients were so nice as to try to stay away from the control room until absolutely necessary so that I don't feel like they watch my every move while as I gather my belongings…"

"Yeah, I imagine that would be awkward…" he agreed.

The Ancients had this uncanny way of making him feel extremely uncomfortable whenever he encountered them; even when he would simply pass them on the corridor, he couldn't help feeling that the way they were looking at him was full of reproach, reminding him that they were unwelcome intruders. He was aware that it could be a bit of an exaggeration, but he really expected a bit more gratitude for the fact that they helped them. If it was anything like this for Elizabeth, he perfectly understood why she decided to use the moment of privacy that they had given her to spend a bit of time in what he knew was one of her favourite spots in the city.

For a moment, they stood on the balcony in complete silence, just staring ahead. It was rather early in their first year in Atlantis that he realized Elizabeth would come out here whenever she was feeling upset, but over time he also learnt that the best way to find out what bothered her was to wait her out. Asking questions, pushing her to talk would never lead to anything different but her shutting him off but if he gave her space, at the same time making her feel that he was there, she would sooner or later open up. He knew that he had accomplished his goal when she let out a heavy sigh and turned to look at him.

"When we were first preparing to come here, I envisioned so many scenarios of how meeting the Ancients would go… I didn't really expect they would welcome us with open arms, we would basically invade their home, after all. But I still hoped that they would let us prove ourselves, show that we're worthy of learning from them and here they are, kicking us out of here…"

"You heard Woolsey. They are willing to let us return one day" he reminded. He knew it wasn't much of a consolation, it definitely didn't make him feel better, but at least it left some kind of hope that they weren't leaving this place forever. The way she looked at him, however, made it rather clear that she wasn't convinced.

"Do you really believe that when the Ancients do agree to let our people back in the city, the IOA will let _us_ come back?" she asked, the irritation audible in her voice. "Did you hear that the Ancients agreed for one person to remain in the city as our Ambassador?" she paused. She must have gotten her answer from the surprised expression that appeared on his face as she didn't wait for him to say anything, just continued. "I'm a diplomat, John. I've worked for our country's government and the United Nations, I've been entrusted with leading the most sensitive of negotiations, including the ones with the System Lords that the safety of our planet depended on, and who does the IOA choose for the job? Richard Woolsey."

John was speechless. He had done his homework when he had first agreed to join the expedition, wanting to know just who he would have to deal with, and that included finding out more about its leader. Back then he was a bit surprised to find out that this strange woman, who struck him as a little obsessed about the fact that he had some kind of a gene that allowed him to operate alien technology, was actually one of the world's best and brightest diplomats. Now, however, as he had got to know her better, he could see the passion, determination and professionalism that would definitely allow her to achieve all that. It seemed like an absurd to him that she wouldn't get the job; he didn't think there could be anyone more fitting for it than her and the more he thought about it, the better he understood her frustration.

"Well, it wouldn't be the first time the IOA shoot itself in the foot… You have every damn right to be pissed, 'Lizbeth. I know I would be. After everything you've done, you're turned down for a position that is practically designed for you and one that would let you stay here. They don't get that for us it's not about losing the chance to explore this city, it's about losing our home."

"Yeah… It's funny to think that just a bit over two years ago I was wondering if I would ever get a chance to see Earth again and now, the sole thought of going back…"

"I know" he said placing a hand on her shoulder and giving it a gentle squeeze. "Anyway, I should probably go to my quarters… I've been going around and harassing people to pack, but I haven't even touched my own stuff… Besides, it seems like our _new_ _friends_ decided you've had enough time" he added, motioning towards the control room with his head and when she looked there, she noticed a few of the Ancients watching the two of them.

"Hmm, going back to quarters seems like a good idea" she said, giving him a small smile. "I just need a moment."

To say goodbye to the city – remained unspoken, but she didn't need to voice the message for him to understand. He just nodded his head and taking one last look at the view spreading in front of him, headed towards the door. It was only when they spread in front of him with a familiar hiss that he stopped, turning around to look at her again.

"Just so that you know, I'm actually glad you're not staying. I'd hate to lose one of my best friends" he said and left before she had a chance to respond.

Slightly taken aback by his statement, she just stood there and watched him walk away until he completely disappeared from her view. A hint of a smile appeared on her face as she processed the words she had to admit that he had a very good point. As much as she loved the place itself, a big part of what made living here such a wonderful experience were the people and it simply wouldn't be the same without them.


End file.
